When populations are facing a climatic change that surpasses their phenotypic plasticity, they either track their ecological niche, genetically adapt to new conditions or collapse. Accurate models of species’ responses to climate changes are essential to inform proper conservation and management actions. The use of genome-wide genetic data enables reconstruction of past demography and detection of the genetic adaptations signal in correlation with the environmental changes. However, the inference based on examination of modern specimens is limited because similar genomic signatures can be produced by different demographic processes and consecutive transitions erase genomic signals of earlier changes. The way to circumvent this limitation is to investigate temporally spaced genetic data obtained from historical and palaeontological specimens, which offers a unique opportunity to directly track changes in the genetic diversity through time. The main goal of this project is to investigate the responses of populations of selected vole (Microtus sp.) species to the Late Glacial and Early Holocene climate and environmental changes using genome-wide genetic data from palaeontological specimens. Voles are a particularly advantageous group to investigate responses to past environmental changes. Their remains are abundant at palaeontological sites and a continuous record spanning multiple climate and environmental oscillations is available. The recent advances in collagen pre-treatment now allows direct radiocarbon dating of minute amounts of bone samples and will provide a high-resolution chronology for the investigated specimens. Most importantly, previous research by the PI revealed that molar teeth of Arvicoline rodents store high amounts of endogenous DNA allowing retrieval of quality genomic data.

However, population-scale genomic analyses from palaeontological material are limited, even despite the recent advanced methodological developments. We will thus first need to develop and optimise a protocol for a cost-effective genotyping of thousands of genomic SNPs from multiple individuals using restriction site associated DNA (ddRAD) as hybridization baits for targeted DNA enrichment. We are planning to investigate three main themes. First will be the reconstruction of the post-glacial history of common (M. arvalis) and field (M. agrestis) vole on the British Isles. Both species have been intensively studied for mitochondrial DNA, but the history of recolonization of British Isles remains uncertain, especially in case of common vole, whose natural presence in this area was confirmed only recently. Investigation of the ancient field vole from the British Isles provides an interesting opportunity as the modern genetic record suggests a complicated history with multiple recolonizations and selection acting as the main factor shaping genetic diversity. We are planning to obtain mtDNA sequences for ca. 50 and genome-wide data for ca. 30 specimens of each species from various sites. We will also generate genomic data for ca. 20 present-day specimens from Western Europe. This combined dataset will enable reconstruction of population dynamics and a search for signatures of selection. The second theme will be a reconstruction of the responses of selected vole species to the Late Glacial and Early Holocene environmental changes in the Western Carpathians. We will obtain genomic data for at least 50 specimens for each of four species: common vole, root vole (M. oeconomus), narrow-headed vole (Lasiopodomys gregalis), and bank vole (Clethrionomys glareolus), from palaeontological sites in Poland, Czechia, Slovakia and

Hungary. These species occupy a range of ecological niches, from dry and cold steppe-tundra to temperate forest and are expected to respond differently to shifts in climatic conditions. Third, we are planning to refine the existing palaeoenvironmental data for the Western Carpathians using metagenomic analyses of cave sediments. This approach well complements palaeovegetation reconstructions based on palynological analyses and, according to the PI’s pilot study, can be successfully applied to cave sediments. Integration of palaeogenomic data from differently adapted species with accurate dating and detailed information on palaeovegetation will provide an opportunity not only for robust recognition of bioclimatic drivers of the population dynamics but also for understanding of their causes and the underlying mechanisms.